10 research outputs found
Conformations of closed DNA
We examine the conformations of a model for a short segment of closed DNA.
The molecule is represented as a cylindrically symmetric elastic rod with a
constraint corresponding to a specification of the linking number. We obtain
analytic expressions leading to the spatial configuration of a family of
solutions representing distortions that interpolate between the circular form
of DNA and a figure-eight form that represents the onset of interwinding. We
are also able to generate knotted loops. We suggest ways to use our approach to
produce other configurations relevant to studies of DNA structure. The
stability of the distorted configurations is assessed, along with the effects
of fluctuations on the free energy of the various configurations.Comment: 39 pages in REVTEX with 14 eps figures. Submitted to Phys. Rev. E.
This manuscript updates, expands and revises, to a considerable extent, a
previously posted manuscript, entitled "Conformations of Circular DNA," which
appeared as cond-mat/970104
Modeling DNA Structure, Elasticity and Deformations at the Base-pair Level
We present a generic model for DNA at the base-pair level. We use a variant
of the Gay-Berne potential to represent the stacking energy between neighboring
base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid
harmonic springs with a non-zero spring length. The competition of these two
interactions and the introduction of a simple geometrical constraint leads to a
stacked right-handed B-DNA-like conformation. The mapping of the presented
model to the Marko-Siggia and the Stack-of-Plates model enables us to optimize
the free model parameters so as to reproduce the experimentally known
observables such as persistence lengths, mean and mean squared base-pair step
parameters. For the optimized model parameters we measured the critical force
where the transition from B- to S-DNA occurs to be approximately . We
observe an overstretched S-DNA conformation with highly inclined bases that
partially preserves the stacking of successive base-pairs.Comment: 15 pages, 25 figures. submitted to PR
Quorum-sensing linked RNA interference for dynamic metabolic pathway control in Saccharomyces cerevisiae
Analyses of DNA from ancient bones of a pre-Columbian Cuban woman and a child
Molecular anthropology has brought new possibilities into the study of ancient human populations. Amplification of chromosomal short tandem repeat (STR) loci and mitochondrial DNA (mtDNA) has been successfully employed in analyses of ancient bone material. Although several studies have reported on continental Amerindian populations, none have addressed the ancient populations inhabiting the Caribbean islands. We used STR and mtDNA analyses to study the skeletal remains of a Cuban Ciboney female adult holding an infant. Results showed that for the STR analyzed the skeletal remains shared common alleles, suggesting a relationship. Mitochondrial DNA analysis showed sequence identity, thus corroborating a possible mother-child relationship. The mtDNA sequence grouped these remains into haplogroup A, commonly found in Amerindian populations. Based on these results, we speculated on a South American origin of pre-Columbian Antilles populations and possible infanticide practices in these populations. This constitutes the first report on DNA analysis of ancient pre-Columbian Cuban populations.<br>A antropologia molecular trouxe novas possibilidades para o estudo de populações humanas antigas. A amplificação de loci em pequenos segmentos cromossômicos repetidos (short tandem repeat, STR) e de DNA mitocondrial (mtDNA) tem sido empregada com sucesso em análises de material ósseo antigo. Embora vários estudos tenham sido publicados a respeito de populações amerÃndias continentais, nenhum estudou as populações antigas que habitavam as ilhas do Caribe. Nós usamos análise de STR e mtDNA para estudar os restos de ossos de uma mulher adulta da tribo Ciboney cubana carregando uma criança. Os resultados mostraram que para o STR analisado os restos ósseos compartilhavam alelos comuns, sugerindo um parentesco. A análise de mtDNA mostrou identidade de seqüência, corroborando assim uma possÃvel relação mãe-filho. A seqüência de mtDNA alocou esses restos no haplogrupo A, comumente encontrado em populações amerÃndias. Baseado nesses resultados, nós especulamos a respeito de uma origem sul-americana para as populações pré-colombianas das Antilhas e possÃveis práticas infanticidas nessas populações. Este constitui o primeiro relato de análise de DNA em populações cubanas pré-colombianas antigas